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Minimum phylogenetic coverage: an additional criterion to guide the selection of microbial pathogens for initial genomic sequenciing efforts

Permanent URL:
http://handle.nal.usda.gov/10113/10362
File:
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Abstract:
The scientific community has made a persuasive case to increase funding for genomic sequencing of microbial plant pathogens, and a number of objective criteria were developed to guide the selection of sequencing targets. However, this task still is complicated for fungi and Oomycetes, which are extremely diverse evolutionarily. Lack of a definite target number of organisms to be sequenced and inclusion of only a small segment of fungal diversity weaken the effort, which may reduce support and hinder efforts to increase the level of funding. These problems can be minimized by inclusion of phylogenetic relationship as an additional criterion to prioritize organisms for genomic sequencing. A phylogenetic analysis of 18S ribosomal DNA sequences revealed that many of the species proposed for genomic sequencing are very closely related, while other evolutionarily important groups, such as the Taphrinales, are under-represented or ignored. By choosing one representative from each of the major clusters on the 18S tree, a minimum phylogenetic coverage (MPC) of the fungi and Oomycetes that have been proposed for genomic sequencing can be achieved by including seven Ascomycetes, four Basidiomycetes, and one Oomycete. A second round of 14 species could be sequenced to cover the major sub-branches within each of the 12 major clusters. This approach defines a tangible, achievable goal for genomic sequencing that could be used to lobby for additional funding. MPC also would assure support and participation by the largest number of plant pathologists because most would have access to a sequenced genome from a close relative of their organism of interest. Allocating funds for this effort might be achieved best through a competitive bidding process among sequencing centers rather than the traditional grants programs. MPC provides a logical criterion to help prioritize fungi, Oomycetes, and other microbial pathogens for genomic sequencing that generates a defined, tractable number of sequencing targets and could serve as a rallying point to unify plant pathologists toward achieving a common goal.
Author(s):
Goodwin, S.B.
Subject(s):
Basidiomycota , Ascomycota , plant pathogenic fungi , phylogeny , genetic variation , nucleotide sequences , experimental design
Format:
p. 800-804.
Note:
Includes references
Source:
Phytopathology 2004 Aug., v. 94, no. 8
Language:
English
Year:
2004
Collection:
Journal Articles, USDA Authors, Peer-Reviewed
Rights:
Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.